Gut microbiome largely stable over time, feces study finds

Human gut microbe

U.S. Department of Agriculture

The bacterium Enterococcus faecalis, one of many that live in the human gut. Just over 10 years ago, it took years to sequence the genome of a single gut microbe. Today, new methods are making the work much faster.

The bacterium Enterococcus faecalis, one of many that live in the human gut. Just over 10 years ago, it took years to sequence the genome of a single gut microbe. Today, new methods are making the work much faster. (U.S. Department of Agriculture)

Eryn Brown

Each of us has a core community of bacterial strains that lives in our lower digestive tract — a personal set of microbes that remains relatively stable in the gut over the course of decades, scientists said Thursday.

In an examination of the bacteria contained in dozens of fecal samples collected from 37 healthy American adults, researchers at the Center for Genome Sciences and Systems Biology at the Washington University School of Medicine in St. Louis found that every person has about 100 species and 200 strains of bacteria in the gut.

On average, 60% of the bacterial strains detected were retained over a period of five years, suggesting that the mix of bacteria in the digestive tract, also known as the gut microbiome, is largely stable.

The work is one of the most extensive to examine changes in the microbiome, experts said.

“This addresses, much more extensively than previous studies, this whole issue of stability, and whether parts of the microbiome persist over time in a single individual,” said Dr. David Relman, a researcher at Stanford University who was not involved in the study. “Much of the published work in the last years put much more attention at looking at many different individuals at one point in time, rather than smaller numbers at many more points in time.”

The human body hosts billions of microbes -- bacteria, fungi and more -- that interact with human cells and help maintain health, affecting our immune systems, our metabolism and maybe more. Scientists want to know whether each person’s gut microbiome changes or remains stable over time so that they can better interpret what shifts in microbial makeup mean, said Washington University biologist Dr. Jeffrey Gordon, senior author of a study describing the research, published Thursday in the journal Science.

“We need to know what normal is to understand what abnormal is,” he said.

Key to generating the new findings, Gordon said, were new methods for identifying the different species lurking in the gut. Computational biologist Jeremiah Faith, a former postdoctoral research scholar in Gordon’s lab who is now running his own laboratory at Mount Sinai Hospital in New York City, designed a more precise way to figure out what bacteria are lurking in a given stool sample.

Rather than isolate all of the bacteria in a sample and culture them to see what’s there, scientists look at the entire community of bacteria at once, focusing on the differences in a single gene in each microbe, 16s rRNA, to separate out the different species that are present.

But there can often be errors in such searches, which can make it hard to figure out exactly what species and strains are in a sample, Faith said. So he figured out a way to get a better read, which lets the team know that the differences they see between microbes are, in fact, differences and not just errors in the data.

Employing Faith’s high-precision technique, the team performed a number of analyses, calculating the numbers of species and strains in each sample, comparing samples from a single individual over time, comparing samples between family members (who had been shown to share microbiomes) and seeing how weight loss or gain affected bacterial makeup, in subjects who were following a special diet as well as subjects who ate as they pleased.

"We found that just by looking at how much the strains have changed, we could estimate how much weight subjects had lost or gained -- you can use microbes as a biomarker" that signals that some change has occurred in the body, Faith said.

The group also performed whole-genome sequencing on 444 bacterial isolates collected from five of the donors, which allowed them to confirm the findings with greater certainty.

They estimated that, were physicians to begin collecting fecal samples to monitor patient health, doing so just once a year would be sufficient to reveal significant changes in the core microbiome. That could provide a useful tool for doctors, Gordon said.

"It appears that because the organisms persist, they have the potential for impacting our physiology for a great deal of our lives -- maybe our entire lives," he said. "Maybe this is part of our biology that is manipulable in ways that will promote health and prevent disease."

Stanford’s Relman, who has also studied how human gut microbiome changes over time, said that understanding stability in microbial communities was “fundamentally important,” and praised the new study as “an important contribution to the story." He agreed that there could be clinical value in monitoring "yearly poop samples" in patients.

At the same time, he said, even with the improved methods, it was still possible that small but significant differences still existed between strains now thought to be identical. Relman also noted that there are many more microbes in other parts of the digestive system about which scientists still don't know much.

Future studies would need to look at how microbial function changes along with microbial populations, he said.

Gordon, who has studied the relationship between gut microbes and obesity, said he was planning to investigate how gut microbiomes develop in healthy children in different parts of the world, as well as how microbes affect nutritional status and metabolism. Faith is studying whether people who have inflammatory bowel diseases, like Crohn's disease, have less stability in their gut microbiomes.

Whatever researchers ultimately discover, having the new technique will make the job much easier than it was when Gordon and colleagues first sequenced the gut microbe Bacteroides thetaiotaomicron. They began the project in 1999 and finished in 2002, publishing their results in Science the following year.

“It took us two and a half years to sequence a single microbial genome,” Gordon said. “A lot has changed.”